Popcorn (Zea mays L.) hybrids grown in the United States are derived from narrow-based germplasm, and standard RFLP analysis detects relatively little polymorphism. Inter-simple sequence repeat (IS S R) amplification, a novel technique based on PCR amplification of inter-microsatellite sequences to target multiple loci in the genome, was employed to investigate its potential for detection of polymorphism among nineteen popcorn and eight dent corn inbred lines. IS SR yielded an average of 54 bands/primer/ inbred line, with over 98 ~o of the bands repeatable across DNA extractions and separate PCR runs. Ten primers based on di-and tri-nucleotide tandem repeats revealed 73?0 and 87~ polymorphism among popcorn and dent corn lines, respectively, with an overall 95?o polymorphism rate. Principal component and cluster analyses resulted in grouping of dent and popcorn lines corresponding to their heterotic breeding pools. ISSR amplification, in addition to being both simple and cost and time efficient, provides for rapid production of highly polymorphic markers which appear to correspond to known pedigree information. Therefore, the ISSR technique may have great potential for identifying polymorphism in species with narrow-based germplasm, and for use in DNA marker-assisted breeding approaches.